OPX Biotechnologies is a bit different than the other companies out there trying to make fuel from microbes.

It's not touting that it's found a magic microbe for turning wood chips into ethanol or synthetic petroleum. In fact, it doesn't even have a microbe in mind yet. Instead, the company has devised a system that speeds up the process for figuring out how the genome in a particular microbe functions and how it can be better exploited.

The tool, developed at the University of Colorado at Boulder, lets researchers test the function of different genes simultaneously. Right now, these tests are conducted sequentially, said CEO Robert Chess. The tool thus radically reduces the time needed to understand how a microorganism functions and therefore lets researchers more rapidly move to the next step, i.e. genetic enhancement and modification.

"It allows you to see everything going on in a microbe at the genetic level and see what causes what to happen," he said.

The company has raised $3.6 million from, among others, Mohr, Davidow Ventures, to now take the tool and develop a microbe capable of spewing out car or jet fuel. Once this is developed, the company would then, ideally, build a prototype manufacturing plant.

It's an interesting approach. Most of the other synthetic biology companies out there--Gevo, LS9, Amyris Biotechnologies--are mostly concentrating on finding the right microbe, not necessarily the tools. (For more on synthetic biology and its adherents, click here.)

So why doesn't OPX just sell the tools? If the software works, it seems that the company would have a built-in customer base. Plus, it's a lot easier to sell software than to find a microorganism that can be coaxed into turning out petroleum. OPX could become the Applied Materials, potentially, of the synthetic bio field.

OPX may license it in a few occasions, but Chess--who is a veteran of the biotech field--says that the most profits can be made by moving closer to the customer. The end product, in other words, will be more profitable.

Developing secret tools for your own personal use actually seems to be a pretty good formula in clean tech. One of the factors that has helped First Solar, the fast-growing solar panel maker, is the fact that it has developed a manufacturing process that no one else has. China's Suntech Power Holdings also is investing heavily in developing its own manufacturing tools.